714 research outputs found
LHC Predictions from a Tevatron Anomaly in the Top Quark Forward-Backward Asymmetry
We examine the implications of the recent CDF measurement of the top-quark
forward-backward asymmetry, focusing on a scenario with a new color octet
vector boson at 1-3 TeV. We study several models, as well as a general
effective field theory, and determine the parameter space which provides the
best simultaneous fit to the CDF asymmetry, the Tevatron top pair production
cross section, and the exclusion regions from LHC dijet resonance and contact
interaction searches. Flavor constraints on these models are more subtle and
less severe than the literature indicates. We find a large region of allowed
parameter space at high axigluon mass and a smaller region at low mass; we
match the latter to an SU(3)xSU(3)/SU(3) coset model with a heavy vector-like
fermion. Our scenario produces discoverable effects at the LHC with only 1-2
inverse femtobarns of luminosity at 7-8 TeV. Lastly, we point out that a
Tevatron measurement of the b-quark forward-backward asymmetry would be very
helpful in characterizing the physics underlying the top-quark asymmetry.Comment: 35 pages, 10 figures, 4 table
Optical Magnetometry
Some of the most sensitive methods of measuring magnetic fields utilize
interactions of resonant light with atomic vapor. Recent developments in this
vibrant field are improving magnetometers in many traditional areas such as
measurement of geomagnetic anomalies and magnetic fields in space, and are
opening the door to new ones, including, dynamical measurements of bio-magnetic
fields, detection of nuclear magnetic resonance (NMR), magnetic-resonance
imaging (MRI), inertial-rotation sensing, magnetic microscopy with cold atoms,
and tests of fundamental symmetries of Nature.Comment: 11 pages; 4 figures; submitted to Nature Physic
Variable DNA methylation in neonates mediates the association between prenatal smoking and birth weight
There is great interest in the role epigenetic variation induced by non-genetic exposures may play in the context of health and disease. In particular, DNA methylation has previously been shown to be highly dynamic during the earliest stages of development and is influenced by in utero exposures such as maternal smoking and medication. In this study we sought to identify the specific DNA methylation differences in blood associated with prenatal and birth factors, including birth weight, gestational age and maternal smoking. We quantified neonatal methylomic variation in 1263 infants using DNA isolated from a unique collection of archived blood spots taken shortly after birth (mean = 6.08 days; s.d. = 3.24 days). An epigenome-wide association study (EWAS) of gestational age and birth weight identified 4299 and 18 differentially methylated positions (DMPs) respectively, at an experiment-wide significance threshold of p < 1 Ă 10-7. Our EWAS of maternal smoking during pregnancy identified 110 DMPs in neonatal blood, replicating previously reported genomic loci, including AHRR. Finally, we tested the hypothesis that DNA methylation mediates the relationship between maternal smoking and lower birth weight, finding evidence that methylomic variation at three DMPs may link exposure to outcome. These findings complement an expanding literature on the epigenomic consequences of prenatal exposures and obstetric factors, confirming a link between the maternal environment and gene regulation in neonates. This article is part of the theme issue 'Developing differences: early-life effects and evolutionary medicine'.This article is freely available via Open Access. Click on the Publisher URL to access it via the publisher's site.This study was supported by grant no. HD073978 from the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Environmental Health Sciences, and National Institute of Neurological Disorders and Stroke; and by the Beatrice and Samuel A. Seaver Foundation. The iPSYCH (The Lundbeck Foundation Initiative for Integrative Psychiatric Research) team acknowledges funding from The Lundbeck Foundation (grant no. R102-A9118 and R155-2014-1724), the Stanley Medical Research Institute, the European Research Council (project no: 294838), the Novo Nordisk Foundation for supporting the Danish National Biobank resource, and grants from Aarhus and Copenhagen Universities and University Hospitals, including support to the iSEQ Center, the GenomeDK HPC facility, and the CIRRAU Center. This research has been conducted using the Danish National Biobank resource, supported by the Novo Nordisk Foundation. J.M. and E.H. are supported by funding from the UK Medical Research Council (K013807).published version, accepted version, submitted versio
Elevated polygenic burden for autism is associated with differential DNA methylation at birth
This is the final version of the article. Available from BioMed Central via the DOI in this record.Autism spectrum disorder (ASD) is a severe neurodevelopmental disorder characterized by deficits in social communication and restricted, repetitive behaviors, interests, or activities. The etiology of ASD involves both inherited and environmental risk factors, with epigenetic processes hypothesized as one mechanism by which both genetic and non-genetic variation influence gene regulation and pathogenesis. The aim of this study was to identify DNA methylation biomarkers of ASD detectable at birth.This study was supported by grant HD073978 from the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Environmental Health Sciences, and National Institute of Neurological Disorders and Stroke; and by the Beatrice and Samuel A. Seaver Foundation. We acknowledge iPSYCH and The Lundbeck Foundation for providing samples and funding. The iPSYCH (The Lundbeck Foundation Initiative for Integrative Psychiatric Research) team acknowledges funding from The Lundbeck Foundation (grant numbers R102-A9118 and R155â2014-1724), the Stanley Medical Research Institute, the European Research Council (project number 294838), the Novo Nordisk Foundation for supporting the Danish National Biobank resource, and grants from Aarhus and Copenhagen Universities and University Hospitals, including support to the iSEQ Center, the GenomeDK HPC facility, and the CIRRAU Center. This research has been conducted using the Danish National Biobank resource, supported by the Novo Nordisk Foundation. JM is supported by funding from the UK Medical Research Council (MR/K013807/1) and a Distinguished Investigator Award from the Brain & Behavior Research Foundation. The SEED study was supported by Centers for Disease Control and Prevention (CDC) Cooperative Agreements announced under the RFAs 01086, 02199, DD11â002, DD06â003, DD04â001, and DD09â002 and the SEED DNA methylation measurements were supported by Autism Speaks Award #7659 to MDF. SA was supported by the Burroughs-Wellcome Trust training grant: Maryland, Genetics, Epidemiology and Medicine (MD-GEM). The SSC was supported by Simons Foundation (SFARI) award and NIH grant MH089606, both awarded to STW
Sialic Acid Glycobiology Unveils Trypanosoma cruzi Trypomastigote Membrane Physiology.
Trypanosoma cruzi, the flagellate protozoan agent of Chagas disease or American trypanosomiasis, is unable to synthesize sialic acids de novo. Mucins and trans-sialidase (TS) are substrate and enzyme, respectively, of the glycobiological system that scavenges sialic acid from the host in a crucial interplay for T. cruzi life cycle. The acquisition of the sialyl residue allows the parasite to avoid lysis by serum factors and to interact with the host cell. A major drawback to studying the sialylation kinetics and turnover of the trypomastigote glycoconjugates is the difficulty to identify and follow the recently acquired sialyl residues. To tackle this issue, we followed an unnatural sugar approach as bioorthogonal chemical reporters, where the use of azidosialyl residues allowed identifying the acquired sugar. Advanced microscopy techniques, together with biochemical methods, were used to study the trypomastigote membrane from its glycobiological perspective. Main sialyl acceptors were identified as mucins by biochemical procedures and protein markers. Together with determining their shedding and turnover rates, we also report that several membrane proteins, including TS and its substrates, both glycosylphosphatidylinositol-anchored proteins, are separately distributed on parasite surface and contained in different and highly stable membrane microdomains. Notably, labeling for Îą(1,3)Galactosyl residues only partially colocalize with sialylated mucins, indicating that two species of glycosylated mucins do exist, which are segregated at the parasite surface. Moreover, sialylated mucins were included in lipid-raft-domains, whereas TS molecules are not. The location of the surface-anchored TS resulted too far off as to be capable to sialylate mucins, a role played by the shed TS instead. Phosphatidylinositol-phospholipase-C activity is actually not present in trypomastigotes. Therefore, shedding of TS occurs via microvesicles instead of as a fully soluble form
Computational methodology to determine fluid related parameters on non regular three-dimensional scaffolds
The application of three-dimensional (3D) biomaterials
to facilitate the adhesion, proliferation, and differentiation
of cells has been widely studied for tissue engineering
purposes. The fabrication methods used to improve the
mechanical response of the scaffold produce complex and
non regular structures. Apart from the mechanical aspect, the
fluid behavior in the inner part of the scaffold should also be
considered. Parameters such as permeability (k) or wall shear
stress (WSS) are important aspects in the provision of
nutrients, the removal of metabolic waste products or the
mechanically-induced differentiation of cells attached in the
trabecular network of the scaffolds. Experimental measurements
of these parameters are not available in all labs.
However, fluid parameters should be known prior to other
types of experiments. The present work compares an
experimental study with a computational fluid dynamics
(CFD) methodology to determine the related fluid parameters
(k and WSS) of complex non regular poly(L-lactic acid)
scaffolds based only on the treatment of microphotographic
images obtained with a microCT (lCT). The CFD analysis
shows similar tendencies and results with low relative
difference compared to those of the experimental study, for
high flow rates. For low flow rates the accuracy of this
prediction reduces. The correlation between the computational
and experimental results validates the robustness of the
proposed methodology.The authors gratefully acknowledge research support from the Spanish Ministry of Science and Innovation through research project DPI2010-20399-C04-01. The Instituto de Salud Carlos III (ISCIII) through the CIBER initiative and the Platform for Biological Tissue Characterization of the Centro de Investigacion Biomedica en Red en Bioingenieria, Biomateriales y Nanomedicina (CIBER-BBN) are also gratefully acknowledged.Acosta SantamarĂa, VA.; MalvĂŠ, M.; Duizabo, A.; Mena Tobar, A.; Gallego Ferrer, G.; GarcĂa Aznar, J.; Doblare Castellano, M.... (2013). Computational methodology to determine fluid related parameters on non regular three-dimensional scaffolds. Annals of Biomedical Engineering. 41(11):2367-2380. https://doi.org/10.1007/s10439-013-0849-8S236723804111Acosta SantamarĂa, V., H. Deplaine, D. MariggiĂł, A. R. Villanueva-Molines, J. M. GarcĂa-Aznar, J. L. GĂłmez Ribelles, M. DoblarĂŠ, G. Gallego Ferrer, and I. Ochoa. Influence of the macro and micro-porous structure on the mechanical behavior of poly(l-lactic acid) scaffolds. J. Non-Cryst. Solids 358(23):3141â3149, 2012.Adachi, T., Y. Osako, M. Tanaka, M. Hojo, and S. J. Hollister. Framework for optimal design of porous scaffold microstructure by computational simulation of bone regeneration. Biomaterials 27(21):3964â3972, 2006.Adamczyk, Z., and T. G. M. Vandeven. Deposition of particles under external forces in laminar-flow through parallel-plate and cylindrical channels. J. Colloid Interface Sci. 80(2):340â356, 1981.Alberich, B. A., D. Moratal, J. L. Escobar, J. C. RodrĂguez, A. VallĂŠs-Lluch, L. MartĂ-BonmatĂ, et al. Microcomputed tomography and microfinite element modeling for evaluating polymer scaffolds architecture and their mechanical properties. J. Biomed. Mater. Res. B Appl. Biomater. 91B(1):191â202, 2009.Al-Munajjed, A., M. Hien, R. Kujat, J. P. Gleeson, and J. Hammer. Influence of pore size on tensile strength, permeability and porosity of hyaluronan-collagen scaffolds. J. Mater. Sci. Mater. Med. 19(8):2859â2864, 2008.Alves da Silva, M. L., A. Martins, A. R. Costa-Pinto, V. M. Correlo, P. Sol, M. Bhattacharya, S. Faria, R. L. Reis, and N. M. Neves. Chondrogenic differentiation of human bone marrow mesenchymal stem cells in chitosan-based scaffolds using a flow-perfusion bioreactor. J. Tissue Eng. Regen. Med. 5(9):722â732, 2011.Ansys (2010) CFX Theory User Manual. Canonsburg, PA: Ansys Software.BrĂgido, R. D., J. M. EstellĂŠs, J. A. Sanz, J. M. GarcĂa-Aznar, and M. S. SĂĄnchez. Polymer scaffolds with interconnected spherical pores and controlled architecture for tissue engineering: fabrication, mechanical properties, and finite element modeling. J. Biomed. Mater. Res. B Appl. Biomater. 81B(2):448â455, 2007.Byrne, P. D., D. Lacroix, J. A. Planell, D. J. Kelly, and P. J. Prendergast. Simulation of tissue differentiation in a scaffold as a function of porosity, Youngâs modulus and dissolution rate: application of mechanobiological models in tissue engineering. Biomaterials 28:5544â5554, 2007.Chor, M. V., and W. Li. A permeability measurement system for tissue engineering scaffolds. Meas. Sci. Technol. 18(1):208â216, 2007.Cozensroberts, C., J. A. Quinn, and D. A. Lauffenburger. Receptor-mediated adhesion phenomenaâmodel studies with the radial-flow detachment assay. Biophys. J. 58(1):107â125, 1990.Davisson, T., R. L. Sah, and A. Ratcliffe. Perfusion increases cell content and matrix synthesis in chondrocyte three-dimensional cultures. Tissue Eng. 8(5):807â816, 2002.Deplaine, H., M. Lebourg, P. Ripalda, A. Vidaurre, P. Sanz-Ramos, G. Mora, F. PrĂłsper, I. Ochoa, M. DoblarĂŠ, J. L. GĂłmez Ribelles, I. Izal-AzcĂĄrate, and G. Gallego Ferrer. Biomimetic hydroxyapatite coating on pore walls improves osteointegration of poly(l-lactic acid) scaffolds. J. Biomed. Mater. Res. B Appl. Biomater. 101(1):173â186, 2013.Dias, M. R., P. R. Fernandes, J. M. Guedes, and S. J. Hollister. Permeability analysis of scaffolds for bone tissue engineering. J. Biomech. 45(6):938â944, 2012.Freyman, T. M., I. V. Yannas, and L. J. Gibson. Cellular materials as porous scaffolds for tissue engineering. Prog. Mater Sci. 46:273â282, 2001.Gong, S., H. Wang, Q. Sun, S. T. Xue, and J. Wang. Mechanical properties and in vitro biocompatibility of porous zein scaffolds. Biomaterials 27(20):3793â3799, 2006.Gutierrez, R. A., and E. T. Crumpler. Potential effect of geometry on wall shear stress distribution across scaffold surfaces. Ann. Biomed. Eng. 36(1):77â85, 2008.Hammer, D. A., and D. Lauffenburger. A dynamic-model for receptor-mediated cell adhesion to surfaces. Biophys. J. 52(3):475â487, 1987.Ho, S. T., and D. W. Hutmacher. A comparison of micro CT with other techniques used in the characterization of scaffolds. Biomaterials 27(8):1362â1376, 2006.Ho, M. H., P. Y. Kuo, H. J. Hsieh, T. Y. Hsien, L. T. Hou, J. Y. Lai, and D. M. Wang. Preparation of porous scaffolds by using freeze-extraction and freeze-gelation methods. Biomaterials 25(1):129â138, 2004.Hutmacher, D. W., J. T. Schantz, C. X. Lam, K. C. Tan, and T. C. Lim. State of the art and future directions of scaffold-based bone engineering from a biomaterials perspective. J. Tissue Eng. Regen. Med. 1(4):245â260, 2007.Izal, I., P. Aranda, P. Sanz-Ramos, P. Ripalda, G. Mora, F. Granero-MoltĂł, H. Deplaine, J. L. GĂłmez-Ribelles, G. G. Ferrer, V. Acosta, I. Ochoa, J. M. GarcĂa-Aznar, E. J. Andreu, M. MonleĂłn-Pradas, M. DoblarĂŠ, and F. PrĂłsper. Culture of human bone marrow-derived mesenchymal stem cells on of poly(l-lactic acid) scaffolds: potential application for the tissue engineering of cartilage. Knee Surg. Sports Traumatol. Arthrosc., 2012.Kapur, S., D. J. Baylink, and K. H. Lau. Fluid flow shear stress stimulates human osteoblast proliferation and differentiation through multiple interacting and competing signal transduction pathways. Bone 32(3):241â251, 2003.Karande, T. S., J. L. Ong, and C. M. Agrawal. Diffusion in musculoskeletal tissue engineering scaffolds: design issues related to porosity, permeability, architecture, and nutrient mixing. Ann. Biomed. Eng. 32(12):1728â1743, 2004.Kelly, D. J., and P. J. Prendergast. Mechano-regulation of stem cell differentiation and tissue regeneration in osteochondral defects. J. Biomech. 38(7):1413â1422, 2005.Kreke, M. R., L. A. Sharp, Y. W. Lee, and A. S. Goldstein. Effect of intermittent shear stress on mechanotransductive signaling and osteoblastic differentiation of bone marrow stromal cells. Tissue Eng. Part A 14(4):529â537, 2008.Lacroix, D., A. Chateau, M. P. Ginebra, and J. A. Planell. Micro-finite element models of bone tissue-engineering scaffolds. Biomaterials 27(30):5326â5334, 2006.Lacroix, D., and P. J. Prendergast. A mechano-regulation model for tissue differentiation during fracture healing: analysis of gap size and loading. J. Biomech. 35(9):1163â1171, 2002.Li, S., J. R. De Wijn, J. Li, P. Layrolle, and K. De Groot. Macroporous biphasic calcium phosphate scaffold with high permeability/porosity ratio. Tissue Eng. 9:535â548, 2003.Melchels, F. P. W., B. Tonnarelli, A. L. Olivares, I. Martin, D. Lacroix, J. Feijen, et al. The influence of the scaffold design on the distribution of adhering cells after perfusion cell seeding. Biomaterials 32(11):2878â2884, 2011.OâBrien, F. J., B. A. Harley, M. A. Waller, I. Yannas, L. J. Gibson, and P. Prendergast. The effect of pore size on permeability and cell attachment in collagen scaffolds for tissue engineering. Technol. Health Care 15(1):3â17, 2007.Ochoa, I., J. A. Sanz, J. M. Garcia-Aznar, M. Doblare, D. M. Yunos, and A. R. Boccaccini. Permeability evaluation of 45S5 bioglass-based scaffolds for bone tissue engineering. J. Biomech. 42:257â260, 2009.Porter, B., R. Zauel, H. Stockman, R. Guldberg, and D. Fyhrie. 3-D computational modeling of media flow through scaffolds in a perfusion bioreactor. Mater. Res. 38:543â549, 2005.Sandino, C., S. Checa, P. J. Prendergast, and D. Lacroix. Simulation of angiogenesis and cell differentiation in a CaP scaffold subjected to compressive strains using a lattice modeling approach. Biomaterials 31(8):2446â2452, 2010.Sanz, J. A., J. M. GarcĂa-Aznar, and M. DoblarĂŠ. On scaffold designing for bone regeneration: a computational multiscale approach. Acta Biomater. 5(1):219â229, 2009.Sanz, J. A., C. Kasper, M. van Griensven, J. M. Garcia-Aznar, I. Ochoa, and M. Doblare. Mechanical and flow characterization of SponceramÂŽ carriers: evaluation by homogenization theory and experimental validation. J. Biomed. Mater. Res. B Appl. Biomater. 87B(1):42â48, 2008.Singh, H., S. H. Teoh, H. T. Low, and D. W. Hutmacher. Flow modelling within a scaffold under the influence of uni-axial and bi-axial bioreactor rotation. J. Biotechnol. 119:181â196, 2005.Sjollema, J., and H. J. Busscher. Deposition of polystyrene latex-particles toward polymethylmethacrylate in a parallel plate flow cell. J. Colloid Interface Sci. 132(2):382â394, 1989.Truscello, S., G. Kerckhofs, S. Van Bael, G. Pyka, J. Schrooten, and H. Van Oosterwyck. Prediction of permeability of regular scaffolds for skeletal tissue engineering: a combined computational and experimental study. Acta Biomater. 8(4):1648â1658, 2012.Woodfield, T. B., J. Malda, J. Wijn, F. PĂŠters, J. Riesle, and C. A. van Blitterswijk. Design of porous scaffolds for cartilage tissue engineering using a three-dimensional fiber-deposition technique. Biomaterials 25(18):4149â4161, 2004
TRY plant trait database - enhanced coverage and open access
Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives
Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV
The performance of muon reconstruction, identification, and triggering in CMS
has been studied using 40 inverse picobarns of data collected in pp collisions
at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection
criteria covering a wide range of physics analysis needs have been examined.
For all considered selections, the efficiency to reconstruct and identify a
muon with a transverse momentum pT larger than a few GeV is above 95% over the
whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4,
while the probability to misidentify a hadron as a muon is well below 1%. The
efficiency to trigger on single muons with pT above a few GeV is higher than
90% over the full eta range, and typically substantially better. The overall
momentum scale is measured to a precision of 0.2% with muons from Z decays. The
transverse momentum resolution varies from 1% to 6% depending on pseudorapidity
for muons with pT below 100 GeV and, using cosmic rays, it is shown to be
better than 10% in the central region up to pT = 1 TeV. Observed distributions
of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO
Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV
The performance of muon reconstruction, identification, and triggering in CMS
has been studied using 40 inverse picobarns of data collected in pp collisions
at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection
criteria covering a wide range of physics analysis needs have been examined.
For all considered selections, the efficiency to reconstruct and identify a
muon with a transverse momentum pT larger than a few GeV is above 95% over the
whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4,
while the probability to misidentify a hadron as a muon is well below 1%. The
efficiency to trigger on single muons with pT above a few GeV is higher than
90% over the full eta range, and typically substantially better. The overall
momentum scale is measured to a precision of 0.2% with muons from Z decays. The
transverse momentum resolution varies from 1% to 6% depending on pseudorapidity
for muons with pT below 100 GeV and, using cosmic rays, it is shown to be
better than 10% in the central region up to pT = 1 TeV. Observed distributions
of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO
Azimuthal anisotropy of charged particles at high transverse momenta in PbPb collisions at sqrt(s[NN]) = 2.76 TeV
The azimuthal anisotropy of charged particles in PbPb collisions at
nucleon-nucleon center-of-mass energy of 2.76 TeV is measured with the CMS
detector at the LHC over an extended transverse momentum (pt) range up to
approximately 60 GeV. The data cover both the low-pt region associated with
hydrodynamic flow phenomena and the high-pt region where the anisotropies may
reflect the path-length dependence of parton energy loss in the created medium.
The anisotropy parameter (v2) of the particles is extracted by correlating
charged tracks with respect to the event-plane reconstructed by using the
energy deposited in forward-angle calorimeters. For the six bins of collision
centrality studied, spanning the range of 0-60% most-central events, the
observed v2 values are found to first increase with pt, reaching a maximum
around pt = 3 GeV, and then to gradually decrease to almost zero, with the
decline persisting up to at least pt = 40 GeV over the full centrality range
measured.Comment: Replaced with published version. Added journal reference and DO
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